Connectome Method

Below, we first show an aggregation of the latest version of FNGS for our respective post-processing pipelines:

  require(Discriminability)

## Loading required package: Discriminability

  signal_overall <- c()
  ids_overall <- c()
  dataset_overall <- c()

FNGS

BNU1 EPI FNIRT

  require(Discriminability)
  inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0530/BNU_1/epi_fnirt/aal-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 2
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)

## [1] "opening timeseries..."

  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal)
  ids_overall <- c(rep('BNU1_epi_fnirt', length(signal)))

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))

## Warning: package 'reshape2' was built under R version 3.3.3

## Warning: package 'ggplot2' was built under R version 3.3.3

#### FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)

## [1] "computing hellinger distances and densities..."

  print(td$combinedplot)

## NULL

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)

## [1] "computing hellinger distances and densities..."

  print(tdr$combinedplot)

## NULL

BNU1 EPI FLIRT

  require(Discriminability)
  inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0530/BNU_1/epi_flirt/aal-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 2
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)

## [1] "opening timeseries..."

  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal)
  ids_overall <- c(rep('BNU1_epi_flirt', length(signal)))

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))

#### FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)

## [1] "computing hellinger distances and densities..."

  print(td$combinedplot)

## NULL

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)

## [1] "computing hellinger distances and densities..."

  print(tdr$combinedplot)

## NULL

BNU1 FLIRT FNIRT

  require(Discriminability)
  inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0530/BNU_1/flirt_fnirt/aal-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 2
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)

## [1] "opening timeseries..."

  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal)
  ids_overall <- c(rep('BNU1_flirt_fnirt', length(signal)))

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))

#### FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)

## [1] "computing hellinger distances and densities..."

  print(td$combinedplot)

## NULL

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)

## [1] "computing hellinger distances and densities..."

  print(tdr$combinedplot)

## NULL

BNU1 FLIRT FLIRT

  require(Discriminability)
  inpath <- 'C:/Users/ebrid/Documents/R/fngs_2mm_0530/BNU_1/flirt_flirt/aal-2mm/'
  tsnames <- list.files(inpath, pattern="\\.rds", full.names=TRUE)
  scan_pos = 2
  tsobj <- open_timeseries(tsnames, sub_pos=scan_pos, exclude = TRUE)

## [1] "opening timeseries..."

  signal <- tsobj[[1]]
  ids <- tsobj[[3]]
  
  signal_overall <- c(signal)
  ids_overall <- c(rep('BNU1_flirt_flirt', length(signal)))

Sanity Check

Timeseries

  ts1 = signal[[1]]
  title = paste('Timeseries plot for subject', ids[1])
  print(plot_timeseries(ts1, title=title))

#### FNGS Correlation Matrix

  title = paste('Correlation plot for subject', ids[1])
  print(plot_square(abs(cor(ts1)), title=title, legend="corr"))

FNGS Raw Correaltion Graphs

  td <- time_discr(signal, ids, rank=FALSE)

## [1] "computing hellinger distances and densities..."

  print(td$combinedplot)

## NULL

FNGS Ranked Correlation Graphs

  tdr <- time_discr(signal, ids, rank=TRUE)

## [1] "computing hellinger distances and densities..."

  print(tdr$combinedplot)

## NULL